Geometric　errors　in　gantry　milling　machines　with　long-span　beams　and　large　travel　can　seriously　degrade　workpiece　accuracy.　Sensitivity　analysis　and　compensation　of　geometric　errors　with　coupling　and　fluctuation　can　significantly　improve　the　machining　performance　of　machine　tools.　An　accuracy　enhancement　approach　for　gantry　milling　machines　is　proposed　in　this　paper.　Firstly,　the　geometry　error　analytic　fluctuation　eigenfunctions　are　established　by　using　the　high-order　Fourier　series　fitting.　Secondly,　a　non-linear　generalized　correlation　analysis　model　is　proposed　to　identify　the　crucial　errors　that　significantly　affect　the　machining　accuracy.　Thirdly,　the　motion　commands　compensated　for　geometric　errors　are　calculated.　Specifically,　compared　to　traditional　inverse　kinematics,　the　proposed　error　compensation　process　is　simple　and　suitable　for　most　machine　tools　with　orthogonal　linear　axes.　Finally,　comparative　cutting　experiments　are　performed.　The　accuracy　of　the　test　piece　is　improved　by　approximately　34.7　%　with　error　compensation.　The　effectiveness　of　the　proposed　method　is　validated.